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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ), 'gf_id' => 'HOM05D001394', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001394' ), 'data_identifier' => 'HOM05D001394', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001394', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '450', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p35340' => 'bna', 'A02p33830' => 'bna', 'A03p41120' => 'bna', 'A03p41130' => 'bna', 'A05p30340' => 'bna', 'A06p09630' => 'bna', 'A08p27200' => 'bna', 'A08p27210' => 'bna', 'A09p62920' => 'bna', 'Aa31LG10G4350' => 'aar', 'Aa31LG1G1340' => 'aar', 'Aa31LG2G6800' => 'aar', 'Aa31LG7G8800' => 'aar', 'Aa31LG8G6050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.2490' => 'aag', 'Actinidia00440' => 'ach', 'Actinidia12949' => 'ach', 'Actinidia18964' => 'ach', 'Actinidia19897' => 'ach', 'Actinidia27957' => 'ach', 'Actinidia31919' => 'ach', 'Actinidia35061' => 'ach', 'Ah.02g127490' => 'amhyb', 'AL1G25320' => 'aly', 'AL1G39550' => 'aly', 'AL3G32660' => 'aly', 'AL5G13950' => 'aly', 'AL5G13980' => 'aly', 'Aqoxy3G00604' => 'aox', 'Aqoxy3G03798' => 'aox', 'Aqoxy5G01237' => 'aox', 'arahy.Tifrunner.gnm1.ann1.26IG8H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.35DV36' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.80KEYX' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E87HJI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FK23LZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FU2LG2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IGY6G6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KKDX05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M69XSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MG7W0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NIGF9J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QN1FMQ' => 'arhy', 'AT1G13580' => 'ath', 'AT1G26200' => 'ath', 'AT3G19260' => 'ath', 'AT3G25540' => 'ath', 'ATR0691G013' => 'atr', 'ATR1102G047' => 'atr', 'Atru.chr11.1517' => 'acertr', 'Atru.chr5.2700' => 'acertr', 'Atru.chr9.682' => 'acertr', 'AUR62003021' => 'cqu', 'AUR62007824' => 'cqu', 'AUR62007825' => 'cqu', 'AUR62023915' => 'cqu', 'AUR62038326' => 'cqu', 'BcaB04g18169' => 'bca', 'BcaB04g19032' => 'bca', 'BcaB04g20714' => 'bca', 'BcaB06g25983' => 'bca', 'BcaB07g29724' => 'bca', 'BcaB08g34313' => 'bca', 'BcaC01g01719' => 'bca', 'BcaC01g01720' => 'bca', 'BcaC01g01721' => 'bca', 'BcaC01g03640' => 'bca', 'BcaC03g17266' => 'bca', 'BcaC05g28507' => 'bca', 'BcaC06g31134' => 'bca', 'BcaC06g31655' => 'bca', 'BcaC06g33982' => 'bca', 'BcaC07g41634' => 'bca', 'BcaC09g48881' => 'bca', 'BcaNung06526' => 'bca', 'BolC1t04452H' => 'bol', 'BolC2t11292H' => 'bol', 'BolC3t17313H' => 'bol', 'BolC3t19558H' => 'bol', 'BolC3t19560H' => 'bol', 'BolC5t29884H' => 'bol', 'BolC5t33310H' => 'bol', 'BolC7t43966H' => 'bol', 'BolC8t52185H' => 'bol', 'BraA01t03615Z' => 'bra', 'BraA02t08401Z' => 'bra', 'BraA03t13269Z' => 'bra', 'BraA05t21872Z' => 'bra', 'BraA06t24154Z' => 'bra', 'BraA08t34666Z' => 'bra', 'BraA08t34667Z' => 'bra', 'BraA09t41650Z' => 'bra', 'C01p44850' => 'bna', 'C02p52070' => 'bna', 'C03p50210' => 'bna', 'C03p72610' => 'bna', 'C03p72640' => 'bna', 'C05p45910' => 'bna', 'C07p34350' => 'bna', 'C08p46360' => 'bna', 'CAN.G1041.12' => 'can', 'CAN.G1305.2' => 'can', 'CAN.G184.16' => 'can', 'CAN.G352.37' => 'can', 'CAN.G667.3' => 'can', 'CAN.G982.27' => 'can', 'CANSAT25G3592' => 'cansat', 'CANSAT64G1860' => 'cansat', 'CANSAT80G2015' => 'cansat', 'CARHR013900' => 'chi', 'CARHR013910' => 'chi', 'CARHR025710' => 'chi', 'CARHR039730' => 'chi', 'CARHR094660' => 'chi', 'CARHR105750' => 'chi', 'CARHR146450' => 'chi', 'Carub.0001s1326' => 'cru', 'Carub.0001s2476' => 'cru', 'Carub.0001s3888' => 'cru', 'Carub.0003s1909' => 'cru', 'Carub.0005s0325' => 'cru', 'Ca_18685_v3' => 'car', 'Ca_22512_v3' => 'car', 'CBR_g48653' => 'cbr', 'CBR_g50435' => 'cbr', 'Cc02_g18800' => 'ccan', 'Cc04_g07950' => 'ccan', 'Cc11_g11210' => 'ccan', 'CDE02G4740' => 'cde', 'CDE03G0237' => 'cde', 'CDE04G2076' => 'cde', 'CDE04G2420' => 'cde', 'CDE04G3468' => 'cde', 'Cfa008826' => 'cfa', 'Cfa022851' => 'cfa', 'Ciclev10021281m.g' => 'ccl', 'Ciclev10021283m.g' => 'ccl', 'Ciclev10027495m.g' => 'ccl', 'Ciclev10027558m.g' => 'ccl', 'Ciclev10028986m.g' => 'ccl', 'Ciclev10032604m.g' => 'ccl', 'CiPaw.05G006700' => 'cil', 'CiPaw.05G119900' => 'cil', 'CiPaw.06G096200' => 'cil', 'CiPaw.06G172400' => 'cil', 'CiPaw.15G117800' => 'cil', 'ClCG01G007400' => 'cla', 'ClCG02G005920' => 'cla', 'COL.COLO4_07846' => 'col', 'COL.COLO4_27748' => 'col', 'COL.COLO4_32655' => 'col', 'Cpa.g.sc53.9' => 'cpa', 'Cpa.g.sc62.10' => 'cpa', 'Cre09.g400516' => 'cre', 'Cre17.g726400' => 'cre', 'CsaV3_5G018870' => 'csa', 'CsaV3_7G008620' => 'csa', 'CSS0005843' => 'camsi', 'CSS0007166' => 'camsi', 'CSS0013751' => 'camsi', 'CSS0020717' => 'camsi', 'CSS0030324' => 'camsi', 'CSS0032519' => 'camsi', 'CSS0037600' => 'camsi', 'CSS0041339' => 'camsi', 'CSS0047656' => 'camsi', 'DCAR_026691' => 'dca', 'DCAR_029057' => 'dca', 'DCAR_030064' => 'dca', 'Dinv08282' => 'din', 'Dinv15560' => 'din', 'Dinv16570' => 'din', 'Dinv36838' => 'din', 'Dinv36839' => 'din', 'Dinv42158' => 'din', 'Duzib052G0202' => 'dzi', 'Duzib132G0032' => 'dzi', 'Duzib205G1203' => 'dzi', 'Duzib248G0165' => 'dzi', 'Duzib248G0526' => 'dzi', 'Duzib251G0136' => 'dzi', 'ECA233G1075' => 'eca', 'ECA234G0459' => 'eca', 'ECA234G0677' => 'eca', 'ECA240G1868' => 'eca', 'EL10Ac9g21103' => 'bvu', 'Eucgr.B03093' => 'egr', 'Eucgr.G01439' => 'egr', 'Eucgr.G01442' => 'egr', 'Eucgr.G02399' => 'egr', 'Eucgr.I01150' => 'egr', 'Eucgr.K00842' => 'egr', 'Eucgr.K02634' => 'egr', 'FAN08G1992' => 'fan', 'FAN12G2698' => 'fan', 'FAN13G1837' => 'fan', 'FAN17G1986' => 'fan', 'FAN18G3151' => 'fan', 'FAN22G0474' => 'fan', 'FvH4_2g06020' => 'fve', 'FvH4_4g28710' => 'fve', 'FvH4_5g13070' => 'fve', 'Glyma.02G126800' => 'gma', 'Glyma.02G127000' => 'gma', 'Glyma.02G132400' => 'gma', 'Glyma.07G212500' => 'gma', 'Glyma.08G269700' => 'gma', 'Glyma.16G091200' => 'gma', 'Gohir.A07G057800' => 'ghi', 'Gohir.A12G024100' => 'ghi', 'Gohir.A12G158200' => 'ghi', 'Gohir.A13G040300' => 'ghi', 'Gohir.A13G096600' => 'ghi', 'Gohir.D07G062600' => 'ghi', 'Gohir.D12G024700' => 'ghi', 'Gohir.D12G161300' => 'ghi', 'Gohir.D13G039000' => 'ghi', 'Gohir.D13G089800' => 'ghi', 'Gorai.001G066100' => 'gra', 'Gorai.008G025000' => 'gra', 'Gorai.008G174300' => 'gra', 'Gorai.013G043800' => 'gra', 'Gorai.013G102900' => 'gra', 'GSVIVG01010169001' => 'vvi', 'GSVIVG01031739001' => 'vvi', 'HanXRQChr08g0214791' => 'han', 'HanXRQChr09g0250401' => 'han', 'HanXRQChr12g0364541' => 'han', 'HanXRQChr16g0528281' => 'han', 'HanXRQChr17g0550791' => 'han', 'Haze_10082' => 'cav', 'Haze_11838' => 'cav', 'HPP92_000492' => 'vpl', 'HPP92_015302' => 'vpl', 'HPP92_018197' => 'vpl', 'HPP92_019152' => 'vpl', 'Hund00337' => 'sun', 'Hund05802' => 'sun', 'Hund06175' => 'sun', 'Hund25135' => 'sun', 'Lalb_Chr05g0219171' => 'lal', 'Lalb_Chr05g0229001' => 'lal', 'Lalb_Chr09g0328331' => 'lal', 'Lalb_Chr10g0099421' => 'lal', 'Lalb_Chr16g0391901' => 'lal', 'Lj2g0008803' => 'lja', 'Lj3A1024T76' => 'lonja', 'Lj4g0003346' => 'lja', 'Lj4g0009983' => 'lja', 'Lj5A209G71' => 'lonja', 'Lj6A771G64' => 'lonja', 'Lj6A771T74' => 'lonja', 'Lj9A436T75' => 'lonja', 'Lj9C358T2' => 'lonja', 'Lsat_1_v5_gn_3_105401' => 'lsa', 'Lsat_1_v5_gn_4_21080' => 'lsa', 'Lsat_1_v5_gn_4_21140' => 'lsa', 'Lsat_1_v5_gn_8_37620' => 'lsa', 'Lsat_1_v5_gn_9_109860' => 'lsa', 'Manes.05G115800' => 'mes', 'Manes.06G077800' => 'mes', 'Manes.07G077800' => 'mes', 'Manes.10G071500' => 'mes', 'Manes.14G093201' => 'mes', 'Mapoly0001s0204' => 'mpo', 'Mapoly0119s0040' => 'mpo', 'Mapoly0154s0016' => 'mpo', 'MBI14_g16234_MAGBIO' => 'mbi', 'MBI15_g03196_MAGBIO' => 'mbi', 'MCO01G405' => 'mco', 'MD00G1035400' => 'mdo', 'MD05G1081300' => 'mdo', 'MD06G1207300' => 'mdo', 'MD09G1247100' => 'mdo', 'MD13G1053200' => 'mdo', 'MD14G1217800' => 'mdo', 'MD16G1052200' => 'mdo', 'Medtr4g086150' => 'mtr', 'Medtr5g049230' => 'mtr', 'Medtr5g049240' => 'mtr', 'Medtr8g069850' => 'mtr', 'MELO3C005172.2' => 'cme', 'MELO3C018448.2' => 'cme', 'Migut.B00348' => 'egut', 'Migut.B00349' => 'egut', 'Migut.E00268' => 'egut', 'Migut.J00253' => 'egut', 'Migut.L01133' => 'egut', 'Migut.N01187' => 'egut', 'MSTRG.13481' => 'ama', 'MSTRG.16744' => 'ama', 'MSTRG.20156' => 'ama', 'MSTRG.2283' => 'ama', 'MSTRG.27726' => 'ama', 'MSTRG.7710' => 'ama', 'Nitab4.5_0000027g0530' => 'nta', 'Nitab4.5_0000149g0120' => 'nta', 'Nitab4.5_0000435g0070' => 'nta', 'Nitab4.5_0000646g0090' => 'nta', 'Nitab4.5_0002097g0020' => 'nta', 'Nitab4.5_0002805g0100' => 'nta', 'Nitab4.5_0004666g0010' => 'nta', 'Nitab4.5_0005249g0070' => 'nta', 'Nitab4.5_0005310g0020' => 'nta', 'Nitab4.5_0010998g0040' => 'nta', 'Nn1g00045' => 'nnu', 'Nn1g04859' => 'nnu', 'Nn2g11849' => 'nnu', 'Nn3g17604' => 'nnu', 'Nn4g23605' => 'nnu', 'Nn5g30318' => 'nnu', 'Oeu006953.2' => 'oeu', 'Oeu010589.1' => 'oeu', 'Oeu024137.1' => 'oeu', 'Oeu025577.1' => 'oeu', 'Oeu025578.1' => 'oeu', 'Oeu054578.1' => 'oeu', 'Os02g0581300' => 'osa', 'Os02g0728300' => 'osa', 'Os03g0264000' => 'osa', 'Os09g0372700' => 'osa', 'Peaxi162Scf00017g03136' => 'pax', 'Peaxi162Scf00152g00020' => 'pax', 'Peaxi162Scf00188g00626' => 'pax', 'Peaxi162Scf00204g00116' => 'pax', 'PGR044G0831' => 'pgr', 'PGR102G1830' => 'pgr', 'PGR119G0419' => 'pgr', 'PGR142G3869' => 'pgr', 'PGSC0003DMG400024613' => 'stu', 'PGSC0003DMG400025120' => 'stu', 'PGSC0003DMG400025796' => 'stu', 'Phvul.003G281100' => 'pvu', 'Phvul.003G292300' => 'pvu', 'Potri.004G141000' => 'ptr', 'Potri.008G113900' => 'ptr', 'Potri.009G101800' => 'ptr', 'Potri.010G134700' => 'ptr', 'Potri.015G055000' => 'ptr', 'Pp3c15_4530' => 'ppa', 'Pp3c15_4537' => 'ppa', 'Pp3c18_640' => 'ppa', 'Pp3c19_9050' => 'ppa', 'Pp3c23_10940' => 'ppa', 'Pp3c4_17010' => 'ppa', 'Pp3c9_8810' => 'ppa', 'PRCOL_00001578' => 'pco', 'PRCOL_00006998' => 'pco', 'Prupe.1G298900' => 'ppe', 'Prupe.5G211700' => 'ppe', 'Prupe.8G125400' => 'ppe', 'Prupe.8G125600' => 'ppe', 'Psat2g098520' => 'psa', 'Psat2g101240' => 'psa', 'Psat4g113400' => 'psa', 'Psat7g124680' => 'psa', 'PSO063G5292' => 'pso', 'PSO478G3498' => 'pso', 'PSO541G4468' => 'pso', 'PSO675G1618' => 'pso', 'PSO782G4193' => 'pso', 'QL03p047819' => 'qlo', 'QL10p021640' => 'qlo', 'QL10p021650' => 'qlo', 'QL10p021665' => 'qlo', 'QL11p035890' => 'qlo', 'RcHm_v2.0_Chr4g0436831' => 'rch', 'RcHm_v2.0_Chr6g0257331' => 'rch', 'RcHm_v2.0_Chr7g0184061' => 'rch', 'Rhsim05G0084500' => 'rsi', 'Rhsim09G0117500' => 'rsi', 'Rhsim12G0069900' => 'rsi', 'Sabra08G0086200' => 'sbr', 'Sabra09G0077800' => 'sbr', 'Sabra10G0103500' => 'sbr', 'Sabra15G0079900' => 'sbr', 'SalBow3G1259' => 'sbo', 'SalBow8G4569' => 'sbo', 'SalBow8G5457' => 'sbo', 'Sc04g0007150' => 'sci', 'Sc18g0004080' => 'sci', 'Sed0015764' => 'sed', 'Sed0019257' => 'sed', 'Sed0021733' => 'sed', 'SEGI_20225' => 'sgi', 'SEGI_28549' => 'sgi', 'SEGI_32534' => 'sgi', 'SEGI_40358' => 'sgi', 'SEGI_40626' => 'sgi', 'SGA_v2.0_scaffold13G06596' => 'sas', 'SGA_v2.0_scaffold14G06780' => 'sas', 'SGA_v2.0_scaffold16G07848' => 'sas', 'SGA_v2.0_scaffold32G13065' => 'sas', 'SGA_v2.0_scaffold59G20642' => 'sas', 'SGA_v2.0_scaffold90G27656' => 'sas', 'SMO118G0419' => 'smo', 'SMO196G0284' => 'smo', 'SMO361G0142' => 'smo', 'Solyc01g108230.3' => 'sly', 'Solyc03g113050.1' => 'sly', 'Solyc03g114600.4' => 'sly', 'Solyc05g010280.3' => 'sly', 'Sopen01g050450' => 'spe', 'Sopen03g032130' => 'spe', 'Sopen03g033670' => 'spe', 'Sopen05g006050' => 'spe', 'Sp1g11960' => 'spa', 'Sp1g22460' => 'spa', 'Sp1g36520' => 'spa', 'Sp2g14800' => 'spa', 'Sp3g17340' => 'spa', 'TAR374G1302' => 'tar', 'TAR381G0303' => 'tar', 'TAR381G0387' => 'tar', 'TAR622G0648' => 'tar', 'TAR625G0201' => 'tar', 'THA.LOC104803454' => 'tha', 'THA.LOC104821980' => 'tha', 'Thecc.02G100900' => 'tca', 'Thecc.02G317800' => 'tca', 'Thecc.03G112400' => 'tca', 'Thhalv10004641m.g' => 'esa', 'Thhalv10008348m.g' => 'esa', 'Thhalv10008634m.g' => 'esa', 'Thhalv10021239m.g' => 'esa', 'TPR.G16494' => 'tpr', 'TPR.G24822' => 'tpr', 'TPR.G25419' => 'tpr', 'TPR.G2664' => 'tpr', 'TPR.G2673' => 'tpr', 'TWI31G0484' => 'twi', 'TWI31G0875' => 'twi', 'TWI73G1292' => 'twi', 'TWI75G0123' => 'twi', 'TWI79G1474' => 'twi', 'unitig_22.g5557' => 'ugi', 'unitig_62.g23704' => 'ugi', 'unitig_744.g24235' => 'ugi', 'vmacro01288' => 'vma', 'vmacro10448' => 'vma', 'vmacro19501' => 'vma', 'VMungo0251G1663' => 'vmu', 'VMungo0251G1699' => 'vmu', 'Zm00001eb011640' => 'zma', 'Zm00001eb098730' => 'zma', 'Zm00001eb183320' => 'zma', 'Zm00001eb245340' => 'zma', 'Zm00001eb253380' => 'zma', 'Zm00001eb311390' => 'zma', 'Zm00001eb398050' => 'zma' ) $gf_id = 'HOM05D001394' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001394' ) $data_identifier = 'HOM05D001394' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 17, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 7, 'amhyb' => (int) 1, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 12, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 5, 'bca' => (int) 18, 'bol' => (int) 9, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 5, 'car' => (int) 2, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 9, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 4, 'bvu' => (int) 1, 'egr' => (int) 7, 'fan' => (int) 6, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 5, 'cav' => (int) 2, 'vpl' => (int) 4, 'sun' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 5, 'mes' => (int) 5, 'mpo' => (int) 3, 'mbi' => (int) 2, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 6, 'ama' => (int) 6, 'nta' => (int) 10, 'nnu' => (int) 6, 'oeu' => (int) 6, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 3, 'pvu' => (int) 2, 'ptr' => (int) 5, 'ppa' => (int) 7, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 4, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 6, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 2, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 7 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb398050' $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